I think it's totally possible that people who own churches and hang those flags, do so as though to say: "this house accepts sinners of all stripes", not, "sin is absolutely okay". The reason for this, I would imagine, is because, although the bible lists a multitude of actions that are offensive to God, for some reason this particular sin is more often fiercely reviled, and those who practice it are shunned and defamed and dehumanized by many churches. Those churches who hang those flags, perhaps have congregations who do not take any more a militant attitude towards homosexuality than they do to say adultery for instance.
I would imagine that very few churches actively practice a doctrine of "being homosexual is acceptable to God", but that those who do hang such flags instead practice a doctrine of "being homosexual is no less acceptable to God than being divorced". There is a difference there. To let gay people know "this is a church where you're welcome, if you want to follow God", is probably helpful for homosexual people to identify the churches they can enter and be treated just the same as any other person who performs a multitude of different actions that are offensive to God. As I understand it, there's nobody who doesn't offend God in some way or other, through their behaviours.